HMRC denies Craig Whyte's suggestion it made an example of Rangers

Craig Whyte issued a lengthy statement in which he criticised HMRC describing it as 'inflexible'. Photograph: Brian Stewart/EPA

Her Majesty's Revenue and Customs has denied any suggestion it has treated Rangers harshly over tax issues. The club have been plunged into administration, leading to a swathe of negative publicity surrounding their running by Craig Whyte, the businessman who bought Rangers from Sir David Murray last May. On Tuesday an embattled Whyte issued a lengthy statement in which he criticised the tax authorities. Whyte claimed HMRC has been "inflexible" and has sought to "make an example" of Rangers.

Rangers are yet to be told the result of a tribunal between themselves and HMRC relating to employee benefit trust payments to staff by the club. It was revealed immediately after the onset of administration that Rangers owed £9m in unpaid VAT and PAYE.

On Wednesday HMRC said: "We can't discuss specific cases for legal reasons, but tax that has been deducted at source from the wages of players and support staff, such as ground keepers and physios, must be paid over to HMRC. Any business that fails to meet that basic legal requirement puts the survival of the business at risk.

"Any business that regards paying tax as an optional extra after other expenses are met, or that uses tax collected from employees or customers as working capital, is potentially heading for trouble.

"There is little HMRC can do for a business – be it a football club or not – whose viability is dependent either on not paying the UK taxes to which they are liable, or on special treatment not available to other customers with similar tax affairs."

Privately HMRC also contests Whyte's claim that the £9m owed is formed partly by a smaller tax case which was apparent prior to his takeover. Rangers' administrators are continuing with complex attempts to find out the full funds available to the club and what level of cuts must be implemented. Staff have been promised they will be paid as scheduled on Thursday.

"Our focus is on generating income for the club, but there is also a focus on costs and the steps we are taking in terms of the cost base of the club will evolve during the next week," said David Whitehouse, Rangers' joint administrator.

Alastair Johnston, the Rangers chairman at the time of Whyte's takeover, has written to the administrators seeking clarification on whether the obligations of that deal have been met. Johnston, who retains more than 150,000 shares in the club, believes Murray has an opportunity to reverse the takeover if guarantees have not been followed through. Crucially, any failings would put at risk Whyte's position as Rangers' secured creditor.

In the letter, Johnston said: "I would request that you investigate and report on the issues pertaining to compliance with Part III, paragraph 1 of the 'Circular to the Shareholders of The Rangers Football Club PLC,' dated June 3, 2011, a copy of which has been previously furnished to you."

"This issue has apparently also been of concern to the vendor because Sir David Murray issued a public statement on February 14 which included the following comment, 'Murray International Holdings wrote to [Whyte's company] Wavetower on 25 August 2011 seeking confirmation that its various obligations were being complied with. A confirmatory assurance was eventually obtained on January 3, 2012. Following recent speculation concerning the financing and security arrangements put in place by Wavetower, a request was issued seeking further clarity.'

"I believe that it would serve the public interest for the administrators to make a full declaration with respect to relevant compliance."